In this work, the case of semantic segmentation on a small image dataset (simulated by 1000 randomly selected images from PASCAL VOC 2012), where only weak supervision signals (scribbles from user interaction) are available is studied. Especially, to tackle the problem of limited data annotations in image segmentation, transferring different pre-trained models and CRF based methods are applied to enhance the segmentation performance. To this end, RotNet, DeeperCluster, and Semi&Weakly Supervised Learning (SWSL) pre-trained models are transferred and finetuned in a DeepLab-v2 baseline, and dense CRF is applied both as a post-processing and loss regularization technique. The results of my study show that, on this small dataset, using a pre-trained ResNet50 SWSL model gives results that are 7.4% better than applying an ImageNet pre-trained model; moreover, for the case of training on the full PASCAL VOC 2012 training data, this pre-training approach increases the mIoU results by almost 4%. On the other hand, dense CRF is shown to be very effective as well, enhancing the results both as a loss regularization technique in weakly supervised training and as a post-processing tool.
Deep learning approaches are nowadays ubiquitously used to tackle computer vision tasks such as semantic segmentation, requiring large datasets and substantial computational power. Continual learning for semantic segmentation (CSS) is an emerging trend that consists in updating an old model by sequentially adding new classes. However, continual learning methods are usually prone to catastrophic forgetting. This issue is further aggravated in CSS where, at each step, old classes from previous iterations are collapsed into the background. In this paper, we propose Local POD, a multi-scale poolin…
Instance segmentation in 3D images is a fundamental task in biomedical image analysis. While deep learning models often work well for 2D instance segmentation, 3D instance segmentation still faces critical challenges, such as insufficient training data due to various annotation difficulties in 3D biomedical images. Common 3D annotation methods (e.g., full voxel annotation) incur high workloads and costs for labeling enough instances for training deep learning 3D instance segmentation models. In this paper, we propose a new weak annotation approach for training a fast deep learning 3D instance …
University of Campinas（坎皮纳斯大学）；Université Gustave Eiffel（古斯塔夫·埃菲尔大学）
Despite the progress of interactive image segmentation methods, high-quality pixel-level annotation is still time-consuming and laborious - a bottleneck for several deep learning applications. We take a step back to propose interactive and simultaneous segment annotation from multiple images guided by feature space projection. This strategy is in stark contrast to existing interactive segmentation methodologies, which perform annotation in the image domain. We show that feature space annotation achieves competitive results with state-of-the-art methods in foreground segmentation datasets: iCoS…
University of Notre Dame（圣母大学）；The Hong Kong Polytechnic University（香港理工大学）；The Chinese University of Hong Kong（香港中文大学）
In recent years, deep learning (DL) methods have become powerful tools for biomedical image segmentation. However, high annotation efforts and costs are commonly needed to acquire sufficient biomedical training data for DL models. To alleviate the burden of manual annotation, in this paper, we propose a new weakly supervised DL approach for biomedical image segmentation using boxes only annotation. First, we develop a method to combine graph search (GS) and DL to generate fine object masks from box annotation, in which DL uses box annotation to compute a rough segmentation for GS and then GS i…
Tackling Ambiguity from Perspective of Uncertainty Inference and Affinity Diversification for Weakly Supervised Semantic Segmentation
Academy for Engineering & Technology, Fudan University（复旦大学工程与技术学院）；Digital Medical Research Center, School of Basic Medical Science, Fudan University（复旦大学基础医学院数字医学研究中心）；Shandong Computer Science Center（山东省计算机科学中心）
Imperial College London（帝国理工学院）；BioMedIA Group, Department of Computing（计算系BioMedIA小组）
Few-shot semantic segmentation (FSS) has great potential for medical imaging applications. Most of the existing FSS techniques require abundant annotated semantic classes for training. However, these methods may not be applicable for medical images due to the lack of annotations. To address this problem we make several contributions: (1) A novel self-supervised FSS framework for medical images in order to eliminate the requirement for annotations during training. Additionally, superpixel-based pseudo-labels are generated to provide supervision; (2) An adaptive local prototype pooling module pl…
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）；Australian Institute for Machine Learning（澳大利亚机器学习研究所）
Manual annotation of medical images is highly subjective, leading to inevitable and huge annotation biases. Deep learning models may surpass human performance on a variety of tasks, but they may also mimic or amplify these biases. Although we can have multiple annotators and fuse their annotations to reduce stochastic errors, we cannot use this strategy to handle the bias caused by annotators' preferences. In this paper, we highlight the issue of annotator-related biases on medical image segmentation tasks, and propose a Preference-involved Annotation Distribution Learning (PADL) framework to …
University of Michigan（密歇根大学）；Indian Institute of Technology - Bombay（印度理工学院孟买分校）
For medical image segmentation, most fully convolutional networks (FCNs) need strong supervision through a large sample of high-quality dense segmentations, which is taxing in terms of costs, time and logistics involved. This burden of annotation can be alleviated by exploiting weak inexpensive annotations such as bounding boxes and anatomical landmarks. However, it is very difficult to \textit{a priori} estimate the optimal balance between the number of annotations needed for each supervision type that leads to maximum performance with the least annotation cost. To optimize this cost-performa…
Technical University of Munich（慕尼黑工业大学）；German Aerospace Center（德国航空航天中心）；Wageningen University（瓦赫宁根大学）；Ecole Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）
Training Convolutional Neural Networks (CNNs) for very high resolution images requires a large quantity of high-quality pixel-level annotations, which is extremely labor- and time-consuming to produce. Moreover, professional photo interpreters might have to be involved for guaranteeing the correctness of annotations. To alleviate such a burden, we propose a framework for semantic segmentation of aerial images based on incomplete annotations, where annotators are asked to label a few pixels with easy-to-draw scribbles. To exploit these sparse scribbled annotations, we propose the FEature and Sp…
Nanyang Technological University（南洋理工大学）；The University of Adelaide（阿德莱德大学）
Weakly supervised semantic segmentation receives much research attention since it alleviates the need to obtain a large amount of dense pixel-wise ground-truth annotations for the training images. Compared with other forms of weak supervision, image labels are quite efficient to obtain. In our work, we focus on the weakly supervised semantic segmentation with image label annotations. Recent progress for this task has been largely dependent on the quality of generated pseudo-annotations. In this work, inspired by spatial neural-attention for image captioning, we propose a decoupled spatial neur…
Challenging computer vision tasks, in particular semantic image segmentation, require large training sets of annotated images. While obtaining the actual images is often unproblematic, creating the necessary annotation is a tedious and costly process. Therefore, one often has to work with unreliable annotation sources, such as Amazon Mechanical Turk or (semi-)automatic algorithmic techniques. In this work, we present a Gaussian process (GP) based technique for simultaneously identifying which images of a training set have unreliable annotation and learning a segmentation model in which the neg…
MPI for Informatics（马克斯·普朗克信息学研究所）；Saarland Informatics Campus（萨尔兰信息学园区）；ETH Zürich（苏黎世联邦理工学院）；CISPA（亥姆霍兹信息安全中心）；MPI for Intelligent Systems（马克斯·普朗克智能系统研究所）；University of Tübingen（蒂宾根大学）
For best performance, today's semantic segmentation methods use large and carefully labeled datasets, requiring expensive annotation budgets. In this work, we show that coarse annotation is a low-cost but highly effective alternative for training semantic segmentation models. Considering the urban scene segmentation scenario, we leverage cheap coarse annotations for real-world captured data, as well as synthetic data to train our model and show competitive performance compared with finely annotated real-world data. Specifically, we propose a coarse-to-fine self-training framework that generate…
University of Notre Dame（圣母大学）；Harper Cancer Research Institute（哈珀癌症研究所）
Image segmentation is a fundamental problem in biomedical image analysis. Recent advances in deep learning have achieved promising results on many biomedical image segmentation benchmarks. However, due to large variations in biomedical images (different modalities, image settings, objects, noise, etc), to utilize deep learning on a new application, it usually needs a new set of training data. This can incur a great deal of annotation effort and cost, because only biomedical experts can annotate effectively, and often there are too many instances in images (e.g., cells) to annotate. In this pap…
Collecting image annotations remains a significant burden when deploying CNN in a specific applicative context. This is especially the case when the annotation consists in binary masks covering object instances. Our work proposes to delineate instances in three steps, based on a semi-automatic approach: (1) the extreme points of an object (left-most, right-most, top, bottom pixels) are manually defined, thereby providing the object bounding-box, (2) a universal automatic segmentation tool like Deep Extreme Cut is used to turn the bounded object into a segmentation mask that matches the extreme…
IIIT Hyderabad（海得拉巴国际信息技术研究所）；University of Oxford（牛津大学）
Recent approaches for weakly supervised instance segmentations depend on two components: (i) a pseudo label generation model that provides instances which are consistent with a given annotation; and (ii) an instance segmentation model, which is trained in a supervised manner using the pseudo labels as ground-truth. Unlike previous approaches, we explicitly model the uncertainty in the pseudo label generation process using a conditional distribution. The samples drawn from our conditional distribution provide accurate pseudo labels due to the use of semantic class aware unary terms, boundary aw…
Recently, weakly-supervised image segmentation using weak annotations like scribbles has gained great attention, since such annotations are much easier to obtain compared to time-consuming and label-intensive labeling at the pixel/voxel level. However, because scribbles lack structure information of region of interest (ROI), existing scribble-based methods suffer from poor boundary localization. Furthermore, most current methods are designed for 2D image segmentation, which do not fully leverage the volumetric information if directly applied to image slices. In this paper, we propose a scribbl…
Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；Carl Zeiss AG（卡尔蔡司公司）；University of Applied Sciences Berlin（柏林应用科学大学）
Pixel-wise segmentation is one of the most data and annotation hungry tasks in our field. Providing representative and accurate annotations is often mission-critical especially for challenging medical applications. In this paper, we propose a semi-weakly supervised segmentation algorithm to overcome this barrier. Our approach is based on a new formulation of deep supervision and student-teacher model and allows for easy integration of different supervision signals. In contrast to previous work, we show that care has to be taken how deep supervision is integrated in lower layers and we present …
When one wants to train a neural network to perform semantic segmentation, creating pixel-level annotations for each of the images in the database is a tedious task. If he works with aerial or satellite images, which are usually very large, it is even worse. With that in mind, we investigate how to use image-level annotations in order to perform semantic segmentation. Image-level annotations are much less expensive to acquire than pixel-level annotations, but we lose a lot of information for the training of the model. From the annotations of the images, the model must find by itself how to cla…
The absence of large scale datasets with pixel-level supervisions is a significant obstacle for the training of deep convolutional networks for scene text segmentation. For this reason, synthetic data generation is normally employed to enlarge the training dataset. Nonetheless, synthetic data cannot reproduce the complexity and variability of natural images. In this paper, a weakly supervised learning approach is used to reduce the shift between training on real and synthetic data. Pixel-level supervisions for a text detection dataset (i.e. where only bounding-box annotations are available) ar…
Imperial College London（帝国理工学院）；The Institute of Cancer Research（英国癌症研究院）；The Royal Marsden NHS Foundation Trust（皇家马斯登国民保健服务基金会信托）
Scarcity of high quality annotated images remains a limiting factor for training accurate image segmentation models. While more and more annotated datasets become publicly available, the number of samples in each individual database is often small. Combining different databases to create larger amounts of training data is appealing yet challenging due to the heterogeneity as a result of differences in data acquisition and annotation processes, often yielding incompatible or even conflicting information. In this paper, we investigate and propose several strategies for learning from partially ov…
EURECOM（法国通信系统工程师学校与研究中心）；Universitat de Barcelona（巴塞罗那大学）；University College London（伦敦大学学院）；Politecnico di Torino（都灵理工大学）；Université Côte d’Azur（蔚蓝海岸大学）；Inria（法国国家信息与自动化研究所）；National Institute for Health Research（英国国家卫生研究院）；University College London Hospitals（伦敦大学学院医院）
Deep learning techniques for 3D brain vessel image segmentation have not been as successful as in the segmentation of other organs and tissues. This can be explained by two factors. First, deep learning techniques tend to show poor performances at the segmentation of relatively small objects compared to the size of the full image. Second, due to the complexity of vascular trees and the small size of vessels, it is challenging to obtain the amount of annotated training data typically needed by deep learning methods. To address these problems, we propose a novel annotation-efficient deep learnin…
Temporally consistent dense video annotations are scarce and hard to collect. In contrast, image segmentation datasets (and pre-trained models) are ubiquitous, and easier to label for any novel task. In this paper, we introduce a method to adapt still image segmentation models to video in an unsupervised manner, by using an optical flow-based consistency measure. To ensure that the inferred segmented videos appear more stable in practice, we verify that the consistency measure is well correlated with human judgement via a user study. Training a new multi-input multi-output decoder using this m…
Deep convolutional neural network (DCNN) is the state-of-the-art method for image segmentation, which is one of key challenging computer vision tasks. However, DCNN requires a lot of training images with corresponding image masks to get a good segmentation result. Image annotation software which is easy to use and allows fast image mask generation is in great demand. To the best of our knowledge, all existing image annotation software support only drawing bounding polygons, bounding boxes, or bounding ellipses to mark target objects. These existing software are inefficient when targeting objec…
German Cancer Research Center (DKFZ)（德国癌症研究中心）；Pallas Ludens GmbH（帕拉斯·卢登斯有限公司）；University Hospital Heidelberg（海德堡大学医院）
With the rapidly increasing interest in machine learning based solutions for automatic image annotation, the availability of reference annotations for algorithm training is one of the major bottlenecks in the field. Crowdsourcing has evolved as a valuable option for low-cost and large-scale data annotation; however, quality control remains a major issue which needs to be addressed. To our knowledge, we are the first to analyze the annotation process to improve crowd-sourced image segmentation. Our method involves training a regressor to estimate the quality of a segmentation from the annotator…
University of Notre Dame（圣母大学）；Guangdong Provincial People’s Hospital（广东省人民医院）
Most existing deep learning-based frameworks for image segmentation assume that a unique ground truth is known and can be used for performance evaluation. This is true for many applications, but not all. Myocardial segmentation of Myocardial Contrast Echocardiography (MCE), a critical task in automatic myocardial perfusion analysis, is an example. Due to the low resolution and serious artifacts in MCE data, annotations from different cardiologists can vary significantly, and it is hard to tell which one is the best. In this case, how can we find a good way to evaluate segmentation performance …
Recent trends in semi-supervised learning have significantly boosted the performance of 3D semi-supervised medical image segmentation. Compared with 2D images, 3D medical volumes involve information from different directions, e.g., transverse, sagittal, and coronal planes, so as to naturally provide complementary views. These complementary views and the intrinsic similarity among adjacent 3D slices inspire us to develop a novel annotation way and its corresponding semi-supervised model for effective segmentation. Specifically, we firstly propose the orthogonal annotation by only labeling two o…
The University of Adelaide（阿德莱德大学）；NVIDIA（英伟达）；Caltech（加州理工学院）；Zhejiang University（浙江大学）
Instance segmentation is a fundamental vision task that aims to recognize and segment each object in an image. However, it requires costly annotations such as bounding boxes and segmentation masks for learning. In this work, we propose a fully unsupervised learning method that learns class-agnostic instance segmentation without any annotations. We present FreeSOLO, a self-supervised instance segmentation framework built on top of the simple instance segmentation method SOLO. Our method also presents a novel localization-aware pre-training framework, where objects can be discovered from complic…
How to Efficiently Annotate Images for Best-Performing Deep Learning Based Segmentation Models: An Empirical Study with Weak and Noisy Annotations and Segment Anything Model
ZScribbleSeg: A comprehensive segmentation framework with modeling of efficient annotation and maximization of scribble supervision
School of Data Science, Fudan University, Shanghai, 200433, China（复旦大学数据科学学院）；Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, USA（约翰霍普金斯大学电气与计算机工程系）
We present a high-performance method that can achieve mask-level instance segmentation with only bounding-box annotations for training. While this setting has been studied in the literature, here we show significantly stronger performance with a simple design (e.g., dramatically improving previous best reported mask AP of 21.1% in Hsu et al. (2019) to 31.6% on the COCO dataset). Our core idea is to redesign the loss of learning masks in instance segmentation, with no modification to the segmentation network itself. The new loss functions can supervise the mask training without relying on mask …
Few-Shot Learning for Annotation-Efficient Nucleus Instance Segmentation
Pazhou Laboratory（琶洲实验室）；Zhujiang Hospital, Southern Medical University（南方医科大学珠江医院）；Nanfang Hospital, Southern Medical University（南方医科大学南方医院）；School of Electronic Information, Wuhan University（武汉大学电子信息学院）；School of Artificial Intelligence and Automation, Huazhong University of Science and Technology（华中科技大学人工智能与自动化学院）；School of Computer Science, Wuhan University（武汉大学计算机学院）
University of British Columbia（不列颠哥伦比亚大学）；University of Nottingham（诺丁汉大学）；Weill Cornell Medicine-Qatar（威尔康奈尔医学院卡塔尔分院）
Semantic image segmentation is one of the most important tasks in medical image analysis. Most state-of-the-art deep learning methods require a large number of accurately annotated examples for model training. However, accurate annotation is difficult to obtain especially in medical applications. In this paper, we propose a spatially constrained deep convolutional neural network (DCNN) to achieve smooth and robust image segmentation using inaccurately annotated labels for training. In our proposed method, image segmentation is formulated as a graph optimization problem that is solved by a DCNN…
National Institutes of Health Clinical Center（美国国立卫生研究院临床中心）；Beijing Institute of Big Data Research（北京大数据研究院）
Image segmentation is a fundamental problem in medical image analysis. In recent years, deep neural networks achieve impressive performances on many medical image segmentation tasks by supervised learning on large manually annotated data. However, expert annotations on big medical datasets are tedious, expensive or sometimes unavailable. Weakly supervised learning could reduce the effort for annotation but still required certain amounts of expertise. Recently, deep learning shows a potential to produce more accurate predictions than the original erroneous labels. Inspired by this, we introduce…
We propose to model complex visual scenes using a non-parametric Bayesian model learned from weakly labelled images abundant on media sharing sites such as Flickr. Given weak image-level annotations of objects and attributes without locations or associations between them, our model aims to learn the appearance of object and attribute classes as well as their association on each object instance. Once learned, given an image, our model can be deployed to tackle a number of vision problems in a joint and coherent manner, including recognising objects in the scene (automatic object annotation), de…
A central challenge for the task of semantic segmentation is the prohibitive cost of obtaining dense pixel-level annotations to supervise model training. In this work, we show that in order to achieve a good level of segmentation performance, all you need are a few well-chosen pixel labels. We make the following contributions: (i) We investigate the novel semantic segmentation setting in which labels are supplied only at sparse pixel locations, and show that deep neural networks can use a handful of such labels to good effect; (ii) We demonstrate how to exploit this phenomena within an active …
National University of Defense Technology（国防科技大学）；National University of Singapore（新加坡国立大学）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
The performance of deep learning based semantic segmentation models heavily depends on sufficient data with careful annotations. However, even the largest public datasets only provide samples with pixel-level annotations for rather limited semantic categories. Such data scarcity critically limits scalability and applicability of semantic segmentation models in real applications. In this paper, we propose a novel transferable semi-supervised semantic segmentation model that can transfer the learned segmentation knowledge from a few strong categories with pixel-level annotations to unseen weak c…
Existing instance segmentation models learn task-specific information using manual mask annotations from base (training) categories. These mask annotations require tremendous human effort, limiting the scalability to annotate novel (new) categories. To alleviate this problem, Open-Vocabulary (OV) methods leverage large-scale image-caption pairs and vision-language models to learn novel categories. In summary, an OV method learns task-specific information using strong supervision from base annotations and novel category information using weak supervision from image-captions pairs. This differen…
Barcelona Supercomputing Center（巴塞罗那超级计算中心）；Universitat Politècnica de Catalunya（加泰罗尼亚理工大学）
Methods that move towards less supervised scenarios are key for image segmentation, as dense labels demand significant human intervention. Generally, the annotation burden is mitigated by labeling datasets with weaker forms of supervision, e.g. image-level labels or bounding boxes. Another option are semi-supervised settings, that commonly leverage a few strong annotations and a huge number of unlabeled/weakly-labeled data. In this paper, we revisit semi-supervised segmentation schemes and narrow down significantly the annotation budget (in terms of total labeling time of the training set) com…
Learning with Limited Annotations: A Survey on Deep Semi-Supervised Learning for Medical Image Segmentation
School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）；School of Data Science, Fudan University（复旦大学大数据学院）；School of Engineering Medicine, Beihang University（北京航空航天大学医工交叉创新研究院）；Artificial Intelligence Innovation and Incubation Institute, Fudan University（复旦大学人工智能创新与产业研究院）；School of Biological Science and Medical Engineering, Beihang University（北京航空航天大学生物与医学工程学院）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）；Beijing Anding Hospital, Capital Medical University（首都医科大学附属北京安定医院）；Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beihang University（北京航空航天大学生物力学与力学生物学教育部重点实验室）；Hefei Innovation Research Institute, Beihang University（北京航空航天大学合肥创新研究院）
Institute of Advanced Research in Artificial Intelligence（高级人工智能研究所）；Helmholtz-Zentrum Dresden-Rossendorf（亥姆霍兹德累斯顿罗森多夫研究中心）；Helmholtz Institute Freiberg for Resource Technology（亥姆霍兹弗赖贝格资源技术研究所）
Deep learning algorithms have obtained great success in semantic segmentation of very high-resolution (VHR) images. Nevertheless, training these models generally requires a large amount of accurate pixel-wise annotations, which is very laborious and time-consuming to collect. To reduce the annotation burden, this paper proposes a consistency-regularized region-growing network (CRGNet) to achieve semantic segmentation of VHR images with point-level annotations. The key idea of CRGNet is to iteratively select unlabeled pixels with high confidence to expand the annotated area from the original sp…
Transformer-based Annotation Bias-aware Medical Image Segmentation
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）；Australian Institute for Machine Learning（澳大利亚机器学习研究所）；Ningbo Institute of Northwestern Polytechnical University（西北工业大学宁波研究院）；Research and Development Institute of Northwestern Polytechnical University in Shenzhen（西北工业大学深圳研究院）
Indian Institute of Technology (BHU) Varanasi（印度理工学院（BHU）瓦拉纳西分校）；Indian Institute of Technology Gandhinagar（印度理工学院甘地讷格尔分校）；Innit Inc.（Innit公司）
Although Deep Convolutional Neural Networks trained with strong pixel-level annotations have significantly pushed the performance in semantic segmentation, annotation efforts required for the creation of training data remains a roadblock for further improvements. We show that augmentation of the weakly annotated training dataset with synthetic images minimizes both the annotation efforts and also the cost of capturing images with sufficient variety. Evaluation on the PASCAL 2012 validation dataset shows an increase in mean IOU from 52.80% to 55.47% by adding just 100 synthetic images per objec…
